To cope with the highly dynamic and uncertain complex combat faced by air-sea integration warfare in the future and counter the increasingly sophisticated anti-missile defense system, an application approach of intelligent penetration technology for missile clusters was proposed. An application framework of intelligent penetration technology for missile clusters was constructed. Then, the key applications of the technology were demonstrated from four aspects: collaborative task planning of ground, collaborative situational awareness, intelligent decision-making, and collaborative penetration and combat. The intelligent penetration methods of missile clusters based on expert systems, neural networks, and group intelligence were reviewed. This study showed that the group intelligence method based on the coordinated driving of knowledge and data had unique advantages in the development of intelligent penetration technology for missile clusters.